CRISPRi-based functional genomic screening identifies genes essential for CH4-dependent growth in a methanotrophic bacterium.

Methanotrophic bacteria are the primary organisms that consume atmospheric methane (CH4) and have potential to mitigate climate-active gases. However, a limited understanding of the genetic determinants of methanotrophy hinders the development of biotechnologies leveraging these unique microbes. Here, we developed and optimized a CRISPR interference (CRISPRi) system to enable functional genomic screening in methanotrophic bacteria. We built a genome-wide single guide RNA (sgRNA) library in the industrial methanotroph, Methylococcus capsulatus, consisting of ~45,000 unique sgRNAs mediating inducible, CRISPRi-dependent transcriptional repression. A selective screen during growth on CH4 identified genes associated with essential methanotrophic bacterial processes and previously unidentified essential gene candidates, highlighting the utility of CRISPRi for functional genetic screening in methanotrophs. The CRISPRi screen also led to nitrate mineral salts medium optimization to improve methanotroph biomass productivity from CH4. Collectively, our results show that the CRISPRi system and sgRNA library developed here can be used for facile gene-function analyses and genomic screening to identify genetic determinants of methanotrophy and isolation of improved methanotroph biocatalysts.